Shallow geothermal energy is a clean and effective form of energy that can overcome the problems associated with the depletion of carbon-based energy carbon emissions. Due to the special hydrogeological conditions in karst regions, the heat transfer between heat exchange boreholes and the ground formation is a complicated, multi-physical process. The abundant groundwater flow plays an important role in the heat transfer process, and even presents an opportunity to mitigate the heat imbalance during the long term operation of ground-coupled heat pumps (GCHP). In this study, both laboratorial experiments and numerical simulations were performed to analyze the mechanism that shows how fracture water impacts on heat capacity and the thermal imbalance of the energy storage rock mass. The results showed that the overall temperature fluctuation of the rock mass was reduced by the fracture water, and the temperature curve with time became gentler, which means in practice that the heat imbalance in the rock mass could be delayed. However, the temperature contour map showed that the impact of the fracture water flow was constrained in the nearby areas and decreased obviously with distance. The temperature field was also dragged along the direction of the fracture water flow. During the shutdown period, the fracture water significantly enhanced the thermal recovery ability of the rock mass. The results will assist in further understanding the mechanism of heat transfer and energy balance in a rock mass with fracture water flow. It is proposed that the U pipes should be located at zones with abundant fracture water if the construction condition permits. U pipes that are near the fractures should share more of the load or a denser layout could be possible as their heat transfer capacity is improved by the water flow.